Directory SL/TREE_READ/

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westram 2022-10-22 19:19 Rev.: 19281

* pull-out {{{parse_treelabel()}}} from {{{setBranchName_acceptingBootstrap()}}}.

7 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+7 -18)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2)

westram 2021-09-15 13:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -2)

westram 2021-09-15 13:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -4)

westram 2021-09-15 13:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -1)

westram 2021-09-15 12:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -2)

westram 2018-10-02 16:08 Rev.: 17428

* partial merge from 'svalues' into 'trunk'
- root branches always need to have identical remarks (associated with the root-edge)
* condition previously implicit, now hardened by tests/assertions/...
* fixed several bugs that violated this condition
* adds: log:branches/svalues@17420:17427

7 lines of code changed in 1 file:

• SL/TREE_READ: TreeTools.cxx (+7 -5)

westram 2018-06-15 13:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

7 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+7 -7)

westram 2018-04-20 13:04 Rev.: 16904

* reintegrates 'pvp' into 'trunk'
- fixes #782
- implements #701
* adds: log:branches/pvp@16882:16903

29 lines of code changed in 2 files:

• SL/TREE_READ: TreeRead.cxx (+27), TreeRead.h (+2 -2)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

45 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+45 -45)

westram 2016-12-17 13:12 Rev.: 15425

* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424

1 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+1 -1)

westram 2016-08-11 11:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2)

westram 2016-03-15 15:54 Rev.: 14697

* avoid too many warning messages of same type (fixes #694)

20 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+20 -3)

westram 2015-03-30 10:28 Rev.: 13639

* full update from child 'pars' into 'trunk'
- cleanup patches
* adds:
- log:branches/pars@13628:13638

1 lines of code changed in 1 file:

• SL/TREE_READ: TreeTools.cxx (+1 -1)

westram 2015-03-29 12:47 Rev.: 13625

* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

77 lines of code changed in 4 files:

• SL/TREE_READ: Makefile (+2), TreeRead.cxx (+69 -55), TreeRead.h (+2 -2), TreeTools.cxx (+4 -3)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2 -2)

westram 2014-01-20 17:08 Rev.: 11488

* reintegrates 'tree' into 'trunk'
- implements #417 (multifurcate tree)
- tree display
* adds MULTIFURC MODE
* reordered modes (synchronizes NTREE and PARSIMONY)
- branch analysis
* display number of multifurcations in 'mark long branches'
* display "in-tree-distance" and "per-species-distance"
- added function to toggle '100%' bootstraps
- document bug in GBT_remove_leafs (#452)
* adds:
- log:branches/tree@11425:11487

18 lines of code changed in 2 files:

• SL/TREE_READ: TreeRead.cxx (+12 -12), TreeTools.cxx (+6 -12)

westram 2013-12-26 13:48 Rev.: 11401

* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

90 lines of code changed in 3 files:

• SL/TREE_READ: TreeRead.cxx (+87 -102), TreeRead.h (+3 -3), TreeTools.cxx (-2)

westram 2013-11-14 19:19 Rev.: 11126

* reintegrates 'redev' into 'trunk':
- fixed tree key-bindings (mark, fold, ...)
- improved several tree-commands (move, rotate, spread, length, width)
- fixed #68
* adds:
- log:branches/dev@7912,7914,7938,7942:7943
- log:branches/redev@11088:11119,11122:11125

15 lines of code changed in 3 files:

• SL/TREE_READ: TreeRead.cxx (+11 -11), TreeRead.h (+2 -3), TreeTools.cxx (+2 -2)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2 -2)

westram 2013-10-29 13:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2 -2)

westram 2013-10-29 12:43 Rev.: 10954

- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -1)

westram 2013-09-09 16:36 Rev.: 10563

- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

3 lines of code changed in 2 files:

• SL/TREE_READ: Makefile (+3), TreeRead.cxx (-1)

westram 2013-09-09 12:55 Rev.: 10557

- rename

4 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+4 -4)

westram 2013-08-25 15:09 Rev.: 10482

* Tree IO (patch reintegrates branch 'tree')
- added unit test (!TreeReader, export/import consistency for most export-parameters combinations)
- refactorings: moved more behavior into !TreeReader; deny access to class internals
- improved error messages/warnings
* show error-position in input data when bailing out
* warn about unused data behind tree
* trees < 2 species produce error now
- behavior
* fixed export/import of bootstrap values (expect ':' as separator; avoiding misinterpretation of group names starting with digits)
* auto-name unnamed nodes
* supports bootstrap values specified as percent (e.g. '12.5%')
* no longer interpret {{{''}}} as escape sequence for a single {{{'}}}
* no longer remove leading '_' from leaf-/groupnames (no idea why this was done)
- fixes:
* export+import of tree using double quotes often resulted in leaf-/groupnames enclosed in double-quotes (or more often failed to load completely)
* name of root-node was lost after import.
* better support for single-node subtrees, e.g. '(leafname)'. Nodes were skipped.
* deadlock occurring when tree file was truncated somewhere in the middle.
* leaks stuffed

812 lines of code changed in 4 files:

• SL/TREE_READ: Makefile (+4), TreeRead.cxx (+799 -268), TreeRead.h (+5 -3), TreeTools.cxx (+4 -4)

aboeckma 2013-08-14 15:09 Rev.: 10445

Allow numbers with positive exponent in newick tree

1 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+1 -1)

westram 2013-07-16 13:50 Rev.: 10284

* valgrinded tree reader
- use GBT_delete_tree (leaked in error case)

4 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+4 -4)

westram 2013-07-16 13:23 Rev.: 10282

* added unit test reading corrupted tree file
- checks for proper failure
- failed till [10278]; succeeds now

19 lines of code changed in 2 files:

• SL/TREE_READ: Makefile (+1), TreeRead.cxx (+18)

westram 2013-07-16 12:45 Rev.: 10280

* GBT_delete_tree
- expects *& as param (value is set to NULL after delete)
- accept NULL as input

1 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+1 -4)

westram 2013-07-16 12:36 Rev.: 10279

* avoid error gets overwritten in !TreeReader (failed assertion in DEBUG mode)
* avoid to free NULL-tree (GBT_delete_tree cant yet)

15 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+15 -11)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

• SL/TREE_READ: Makefile (+2)

westram 2012-11-15 17:12 Rev.: 9170

merge from stable_5.0 [9163] [9164] [9166]

0 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (changed)

westram 2012-10-25 15:04 Rev.: 9080

* reverted [9079], instead explain how to undo auto-scaling

7 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+7 -5)

westram 2012-10-25 13:52 Rev.: 9079

- ~~autoscale if branch lengths are > 3.0~~

(reverted by [9080])

3 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (+3 -4)

westram 2012-05-11 12:32 Rev.: 8725

* comments cleanup

0 lines of code changed in 1 file:

• SL/TREE_READ: TreeRead.cxx (-1)

westram 2012-04-11 13:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

• SL/TREE_READ: needs_libs (+1 -1)

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